Significance Monitoring and controlling the genetic structure of non-human primate breedingcolonies and reconstructing/confirming genealogical relationships in the colonies are essential to the maintenance of non-human primates as a research resource. Objectives This study aims to develop rapid and inexpensive methods to conduct paternity exclusion analysis and estimate kinship, inbreeding and gene diversity in groups of non-human primates. Results The six most informative of thirteen human microsatellite (STR) loci found to be highly polymorphic in rhesus macaques were employed for paternity exclusion analysis (PEA) in 11 multimale groups of rhesus macaques and one captive group of Papio hamadryas hamadryas. STR loci were amplified by the polymerase chain reaction using human primers. The success of PEA in rhesus was slightly greater than predicted, leading to identification of the sires of 216 of 224 offspring. The sires of all 25 baboons born in the group studied were identified using these loci. Moreover, about half the offspring were sired by leader males outside their damms harem group suggesting that only the highest ranking males are able to monopolize sexual access to the females in their harem when they number as high as 5 females. More surprising, the alleged dams of 12 of the 25 offspring were excluded from maternity. STR loci are important because they permit PEA without needing to assume that the alleged dam is in fact the true dam and usually allow the identification of the true dam. Future Directions The STR loci cited above will be used to screen a variety of other cercopithecoid species including patas, vervet, and howler monkeys and orangutans to assess their effectiveness for genetic management, and mother/offspring pairs of rhesus in the 11 rhesus groups described above will be screened for all 13 STR loci to estimate the incidence of mistaken maternity in rhesus groups. KEYWORDS microsatellite (STR) loci, PCR amplification, paternity exclusion analysis (PEA)